title: Genetic and microbial factors modulating the ubiquitin proteasome system in inflammatory bowel disease.
abstract: OBJECTIVE
  Altered microbiota composition, changes in immune responses and impaired intestinal barrier functions are observed in IBD. Most of these features are controlled by proteases and their inhibitors to maintain gut homeostasis. Unrestrained or excessive proteolysis can lead to pathological gastrointestinal conditions. The aim was to validate the identified protease IBD candidates from a previously performed systematic review through a genetic association study and functional follow-up.
  
  
  METHODS
  We performed a genetic association study in a large multicentre cohort of patients with Crohn's disease (CD) and UC from five European IBD referral centres in a total of 2320 CD patients, 2112 UC patients and 1796 healthy controls. Subsequently, we did an extensive functional assessment of the candidate genes to explore their causality in IBD pathogenesis.
  
  
  RESULTS
  Ten single nucleotide polymorphisms (SNPs) in four genes were significantly associated with CD: CYLD, USP40, APEH and USP3. CYLD was the most significant gene with the intronically located rs12324931 the strongest associated SNP (p(FDR)=1.74e-17, OR=2.24 (1.83 to 2.74)). Five SNPs in four genes were significantly associated with UC: USP40, APEH, DAG1 and USP3. CYLD, as well as some of the other associated genes, is part of the ubiquitin proteasome system (UPS). We therefore determined if the IBD-associated adherent-invasive Escherichia coli (AIEC) can modulate the UPS functioning. Infection of intestinal epithelial cells with the AIEC LF82 reference strain modulated the UPS turnover by reducing poly-ubiquitin conjugate accumulation, increasing 26S proteasome activities and decreasing protein levels of the NF-κB regulator CYLD. This resulted in IκB-α degradation and NF-κB activation. This activity was very important for the pathogenicity of AIEC since decreased CYLD resulted in increased ability of AIEC LF82 to replicate intracellularly.
  
  
  CONCLUSIONS
  Our results reveal the UPS, and CYLD specifically, as an important contributor to IBD pathogenesis, which is favoured by both genetic and microbial factors.
authors.affiliation: Department of Clinical and Experimental Medicine, TARGID, KU Leuven, Leuven, Belgium.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Cleynen
authors.affiliation: Clermont Université, Inserm U1071, Université d'Auvergne, INRA USC 2018, Clermont-Ferrand, France Centre Hospitalier Universitaire, Clermont-Ferrand, France.
authors.forename: Emilie
authors.initials: E
authors.lastname: Vazeille
authors.affiliation: Progenika Biopharma, S.A., Derio, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Artieda
authors.affiliation: Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands Dutch Initiative on Crohn and Colitis (ICC).
authors.forename: Hein W
authors.initials: HW
authors.lastname: Verspaget
authors.affiliation: Progenika Biopharma, S.A., Derio, Spain.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Szczypiorska
authors.affiliation: Clermont Université, Inserm U1071, Université d'Auvergne, INRA USC 2018, Clermont-Ferrand, France.
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Bringer
authors.affiliation: 1st Department of Medicine, Semmelweis University, Budapest, Hungary.
authors.forename: Peter L
authors.initials: PL
authors.lastname: Lakatos
authors.affiliation: Department of Gastroenterology, Spitalnetz Bern, Switzerland.
authors.forename: Frank
authors.initials: F
authors.lastname: Seibold
authors.affiliation: Peninsula Medical School, University of Exeter & Plymouth, Exeter, UK.
authors.forename: Kirstie
authors.initials: K
authors.lastname: Parnell
authors.affiliation: Dutch Initiative on Crohn and Colitis (ICC) Department of Gastroenterology and Hepatology, University Medical Center Groningen and the University of Groningen, Groningen, The Netherlands.
authors.forename: Rinse K
authors.initials: RK
authors.lastname: Weersma
authors.affiliation: Systems and Modeling Unit, Montefiore Institute, University of Liège, Liège, Belgium Bioinformatics and Modeling, GIGA-R, University of Liège, Liège, Belgium.
authors.forename: Jestinah M
authors.initials: JM
authors.lastname: Mahachie John
authors.affiliation: Clinical and Experimental Sciences, Faculty of medicine, University of Southampton, Southampton, UK.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Morgan-Walsh
authors.affiliation: Department of Clinical and Experimental Medicine, TARGID, KU Leuven, Leuven, Belgium.
authors.forename: Dominiek
authors.initials: D
authors.lastname: Staelens
authors.affiliation: Department of Clinical and Experimental Medicine, TARGID, KU Leuven, Leuven, Belgium.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Arijs
authors.affiliation: Department of Morphology and Molecular Pathology, University Hospital Gasthuisberg, Leuven, Belgium.
authors.forename: Gert
authors.initials: G
authors.lastname: De Hertogh
authors.affiliation: Department of Clinical Research, University of Bern, Bern, Switzerland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Müller
authors.affiliation: Hungarian National Blood Transfusion Service, Molecular Diagnostics, Budapest, Hungary.
authors.forename: Atilla
authors.initials: A
authors.lastname: Tordai
authors.affiliation: Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands Dutch Initiative on Crohn and Colitis (ICC) Division of Digestive Diseases, Inflammatory Bowel Diseases Center, UCLA, Los Angeles, USA.
authors.forename: Daniel W
authors.initials: DW
authors.lastname: Hommes
authors.affiliation: Peninsula Medical School, University of Exeter & Plymouth, Exeter, UK.
authors.forename: Tariq
authors.initials: T
authors.lastname: Ahmad
authors.affiliation: Dutch Initiative on Crohn and Colitis (ICC) Department of Genetics, University Medical Center Groningen and the University of Groningen, Groningen, The Netherlands.
authors.forename: Cisca
authors.initials: C
authors.lastname: Wijmenga
authors.affiliation: Clinical and Experimental Sciences, Faculty of medicine, University of Southampton, Southampton, UK.
authors.forename: Sylvia
authors.initials: S
authors.lastname: Pender
authors.affiliation: Department of Clinical and Experimental Medicine, TARGID, KU Leuven, Leuven, Belgium.
authors.forename: Paul
authors.initials: P
authors.lastname: Rutgeerts
authors.affiliation: Systems and Modeling Unit, Montefiore Institute, University of Liège, Liège, Belgium Bioinformatics and Modeling, GIGA-R, University of Liège, Liège, Belgium.
authors.forename: Kristel
authors.initials: K
authors.lastname: Van Steen
authors.affiliation: Department of Rheumatology, Clinical Immunology and Allergology, University Hospital of Bern, Inselspital, Switzerland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Lottaz
authors.affiliation: Department of Clinical and Experimental Medicine, TARGID, KU Leuven, Leuven, Belgium.
authors.forename: Severine
authors.initials: S
authors.lastname: Vermeire
authors.affiliation: Clermont Université, Inserm U1071, Université d'Auvergne, INRA USC 2018, Clermont-Ferrand, France Centre Hospitalier Universitaire, Clermont-Ferrand, France.
authors.forename: Arlette
authors.initials: A
authors.lastname: Darfeuille-Michaud
mesh_terms: D001422:Bacterial Adhesion; D016022:Case-Control Studies; D002470:Cell Survival; D002478:Cells, Cultured; D003093:Colitis, Ulcerative / Q000201:enzymology / Q000235:genetics* / Q000382:microbiology; D003424:Crohn Disease / Q000201:enzymology / Q000235:genetics* / Q000382:microbiology; D000074749:Deubiquitinating Enzyme CYLD; D049030:Dystroglycans / Q000235:genetics; D004847:Epithelial Cells / Q000201:enzymology* / Q000382:microbiology; D004926:Escherichia coli / Q000472:pathogenicity; D056726:Genetic Association Studies; D006801:Humans; D020672:I-kappa B Proteins / Q000378:metabolism; D007413:Intestinal Mucosa / Q000382:microbiology; D016328:NF-kappa B / Q000378:metabolism; D010447:Peptide Hydrolases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism; D025521:Tumor Suppressor Proteins / Q000235:genetics / Q000378:metabolism*; D043222:Ubiquitin Thiolesterase / Q000235:genetics; D064570:Ubiquitin-Specific Proteases / Q000235:genetics
chemical_list: C483081:DAG1 protein, human; D020672:I-kappa B Proteins; D016328:NF-kappa B; D025521:Tumor Suppressor Proteins; C513808:USP40 protein, human; D049030:Dystroglycans; D010447:Peptide Hydrolases; C038220:acylaminoacyl-peptidase; C409984:CYLD protein, human; D000074749:Deubiquitinating Enzyme CYLD; C579221:USP3 protein, human; D043222:Ubiquitin Thiolesterase; D064570:Ubiquitin-Specific Proteases; D046988:Proteasome Endopeptidase Complex; C061553:ATP dependent 26S protease
keywords: BACTERIAL PATHOGENESIS; IBD - GENETICS; IBD BASIC RESEARCH; INFLAMMATORY BOWEL DISEASE; MOLECULAR GENETICS